The battle begins
by honour632
Summary: Tony and Ziva are put on a dangerous mission together. They have just started dating too and will the danger bring them to another level for their relanship?
1. Chapter 1

**This story at the end of season 9 when Tony and Ziva are stuck in the elevator after the explosion. Hope you enjoy.**

"It's getting really stuffy in here." Tony whined. Ziva just scoffed and rolled her eyes.

"This is nothing compared to the heat you get in Israel so stop whining." Ziva said.

"Well, we're not in Israel at the moment are we?" Tony rolled his eyes. Typical Ziva, always annoying him. All of a sudden the elevator shock and fell a few inches. Ziva latched onto Tony and Tony latched onto her.

"What was that?" Ziva asked.

'I don't know." Tony replied, turning his head to look at her. She looked up at him and stared straight into his eyes. Something in Tony's eyes made Ziva kiss him. He was shocked at first, but after a few seconds he kissed her back. They kissed for a few minutes until they heard the elevator doors creak.

They immediately let go of each other and when the doors were opened, they pretended as if the kiss hadn't happened.

"Abby, I have never been happier to see your beautiful bright face." Ziva exclaimed. She was going to have to watch what she said from now on. She didn't want to give away the kiss.

Tony smiled and jumped out of the half opened doors. Once he was out, he helped Ziva out and then turned to Abby.

"Is everyone okay?" He asked. Abby's face fell.

"Ducky had a heart attack and is in hospital. Jimmy's with him. A lot of people have died today. I was just glad that Gibbs was with me when the bomb went off." Abby said as she hugged Ziva.

"Have you heard from McGee?" Ziva asked and Abby's face fell even more.

"No. I haven't. he was upstairs when the bomb blew so Gibbs is up there looking for him." Abby said. All of a sudden, her phone rang and she put it on loudspeaker.

"Gibbs, have you found Timmy?" Abby asked. Only she could call McGee Timmy and get away with it (except for Tim's family).

_"Yea. He was hit with a piece of glass in the stomach. He's okay, but he's at the hospital. He got three stiches."_ Gibbs told her. Abby gasped.

"Is he okay?" She asked.

_"I'm fine. Just tired." _McGee called out from the background. The three of them sighed when they heard his voice and then they said goodbye and hung up.

"I had better start cleaning up my lab." Abby said and she turned towards the stairs, going down one level to where the laboratories were.

When Tony and Ziva were alone again they talked about the kiss.

"I've wanted to do that for so long." Tony said.

"Really?" Ziva asked. She stared straight up at him and then smiled.

"What?" Tony asked, turning to look behind him, thinking Gibbs was standing there.

"Nothing. It's just the way the sun shines through the window and makes your hair look really bright." Ziva said. she looked down to the floor. She had never been good at expressing her emotions before, but she found it easy with Tony. He smiled back at her and then hugged her. He was about to lean in for another kiss when Vance, the director of NCIS, walked in.

"Tony, Ziva, I have a proposition for you. As soon as this case is over, I have a special mission for you two. It will mean that you won't be able to get in touch with your colleagues as much, but the job needs to be done." Vance said, looking straight at the two of them.

"What would this special mission involve exactly?" Tony asked.

"Well, there are some drug dealers and illegal weapon handlers that need to be dealt with. Can I have your full co-operation with this?" Vance asked them, lowering his head, but keeping full eye contact with them.

"I'm in. Are you?" Ziva asked Tony, staring at him. She hoped that he would say yes. She didn't want to go with anyone else.

"I'm in." Tony said after he tore his eyes from Ziva's. Vance nodded and smiled. He knew that something was going on between them and that's why he picked them. He knew they worked best together.

A few days after they had caught the guy who had blown up the NCIS building, Ziva and Tony took off for their mission. They were now in a secret relationship and they were planning to keep it that way.

Gibbs wasn't very happy about them leaving, but he dealt with it and got two stand in's. Dournaget was one of them, a junior agent, and the other one was a new recruit that Vance wanted to start off in the field. Gibbs and McGee soon learnt to work cooperatively with them.

Tony and Ziva however, where in a slight trouble after a week of leaving. A drug dealer had escaped them and was now after them. They were good at hiding though. Tony had managed to get in contact with McGee for a few minutes and got him to send some personal files through.

"What's in the files?" Ziva asked once McGee and Tony were off of the phone. Tony was sitting at his laptop. He opened one of the files and a heap of passports popped up. Ziva looked through them and saw that there was one for everyone that Tony loved. There was one for Gibbs, Abby, Ziva, McGee, Ducky, Palmer, Palmers wife Breena and her dad and then his dad. There was even one for Dournaget and Vance and his family.

"Where did you get all of these?" Ziva asked as Tony picked the first two passports of Ziva's and Tony's.

"I had them made a few months ago just in case. I made some for Vance's family and when I showed him he was very thankful. He got them off of me and now he holds them with him at all times." Tony replied. He printed the passports off of the laptop to the small printer they had gotten. He then got out two new passport cases and stuck the right papers in the right case.

"How do you know how to make those?" Ziva asked as she took a sip of her coffee.

"I learnt how to make them when I was a cop in Baltimore. I had to change my name for a few weeks because some crazy murderer was after me." Tony said. "The guy was caught." He quickly added after he saw the look of Ziva's face.

Ziva relaxed a little and then sat on his lap. She kissed him and then they heard yelling coming from the hall. They grabbed their guns and then stood up, hiding from sight. The yelling soon died off and they both relaxed, but a few seconds later a gunshot echoed through the wall. Tony yelled out.

The bullet had gone through the wall he was standing near and had hit him in the arm.

"TONY!" Ziva yelled, running over to him to see if he was okay. He had his hand on the gun still though and he opened the door. He shot his gun three times and then walked over to the body that was now dead.

"Are you okay?" Ziva asked Tony once he had made sure the guy he had shot was dead. The only reason he had shot him was because he was the drug dealer that was after him. The guys phone buzzed suddenly and Ziva picked it up.

This is what it said:

_There is nowhere to run. We will all find you for killing our leader. You will suffer for what you have done._

Ziva showed the message to Tony who grabbed all of their stuff and shoved it into their bags.

"We need to get out of here. And now." He said. Ziva knew that this was the beginning of a war between the good and bad and she didn't like the consequences.


	2. Chapter 2

For the next few days, Tony and Ziva were constantly on the move. They changed hotels every night, using different names each time. One night, after Tony and Ziva had settled into their fifth hotel that week, they sat on the couch. Ziva was shaking a little. She had never been this scared. Tony tried his best to comfort her but Ziva knew he was just as scared, maybe even more.

"I don't want to die." She whispered into his shoulder.

"You're not going to die and neither am I. We are going to make it out alive." Tony said to her, making her look into his eyes. She sat there staring into his eyes until something in her snapped. Everything happened so quickly in that instant. One minute they were sitting on the couch and the next they were tearing each other's clothes off in the bedroom and going for it.

She couldn't believe that it had happened when she woke up the next morning. She looked around her to see if it was true and when she saw a sleeping Tony, she smiled. She got dressed and went into the kitchen, making herself some breakfast. She had barely put her begun to spread her toast when Tony came out.

"Morning." He said, going up to her and hugging her from behind. He kissed he cheek and she smiled.

"Morning." She said. She had barely had time to say anymore when they heard gunshots coming from the street. They packed everything they had and got the hell out of there. They managed to get to airport before the shooters caught up with them. Ziva saw them first. Three men with black jackets on were coming in through three different doors. She elbowed Tony who turned just as the three men spotted them. Tony and Ziva quickly ducked out of sight and headed towards the private plane they were taking.

They managed to get onto the plane, but as the doors were closing, gunshots blasted around them from a machine gun. They hid out of sight from the windows and when the plane took off, the gunshots stopped. Tony and Ziva sat on the floor for a few more minutes until they were safe.

"That was too close for my liking." Tony sat leaning back into the cushion of the chair he sat in.

"I've had a guy closer, but yes, that was too close." Ziva said, sitting down next to him. She took his hand and then looked into his eyes.

"I love you." Tony suddenly said. Ziva was taken by surprise but it didn't take any longer than a few seconds to answer him.

"I love you too." She replied and then they kissed. "I never want to lose you." She said.

"Me either. About you obviously." Tony replied. Ziva laughed and then she grabbed some water and soon fell asleep on Tony's shoulder.

Tony and Ziva travelled in that plane for five months. They stopped every few days to get new supplies and other things, but they never stayed on the ground for more than three hours at a time.

Ziva and Tony had a major problem though. Ziva had found out that she was pregnant. Travelling had become difficult for her because she kept getting sick. She couldn't keep anything down half of the time. In the end Tony would make sure one of the bodyguards were on the plane with her at all times if he was to leave the plane.

Ziva was surprised about Tony's reaction. He wasn't overly thrilled but that was because of what kind of positions they were in, being chased and all that. Other than that, he was really happy about it and he was always helping Ziva do everything. She loved the attention, but when they landed in D.C. she worried about running into Gibbs at the office.

They had decided that it was time to see everyone and they needed to speak to Vance anyway. When they got to the office, they made sure that no one knew who they were by covering up their faces and walking straight past them to Vance's office.

"They look familiar." Dournaget said as they passed them and Tony fastened his pace.

"Wait, how did they get past security?" the new recruit asked. McGee suddenly knew who it was and yelled out their names.

"Tony, Ziva, is that you?" McGee called out. Tony and Ziva stopped. They turned and they were glad to find that Ziva wearing Tony's jacket hid the fact that Ziva was pregnant.

"When did you get back?" McGee asked. He was pleased to see his old friends.

"About an hour ago." Ziva said. She still wasn't feeling very well and Tony could see it so he told her to sit down.

"What's wrong with her?" Dournaget asked.

"I'm just not feeling very well." Ziva replied. At that moment, Gibbs came into the office. When he got to his team, he seemed confused as to why there was five people standing there, but when he realised that Tony and Ziva were there, he smiled.

"I thought you were on a mission." He said, smirking slightly.

"We are. We're in hiding though. Killed a drug dealer and now his gang is after us." Tony said, laughing the way he usually did when he said those kinds of things.

"How come you're here then?" the new recruit asked. Ziva looked straight to the new recruit.

"Whose this?" Ziva asked.

"I'm probationary agent Hagger. I was filling in for you when you weren't here." He said. He shook Tony's hand, but when he went to shake Ziva's, she glared at him making him back away quickly.

A few seconds later, Abby, Palmer and Ducky came up with reports for the case that Gibb's team was working on.

"Gibbs, Gibbs, you'll never believe what Ducky and Palmer found on the body." She said. She turned around to get the screen working when she saw Ziva and Tony.

"Oh my gosh. When did you get here?" She asked hugging them. "Is Ziva okay? She looks really pale." Abby said after she had let go of her and Tony.

"She's not feeling well." Tony said for Ziva. Ziva suddenly sat down again and put her head in her hands.

"Ziva are you okay?" Abby asked again.

"Yea. I'm just a little dizzy." Ziva said. Abby didn't believe her, but she turned back to what she had been telling Gibbs.

"Anyway, as I was saying, Ducky and Palmer found minute traces of radioactivity. However, the body was found a garbage dump 20 miles from any radioactive sites. This body was either working with radioactive things or he was trying to get something from there and was killed then dumped." Abby was full of energy as she spoke (as usual).

"That's not all we found. We also found traces of gunpowder residue and hair." Palmer said. His face fell slightly as he spoke, making everyone wonder.

"Who does the hair belong to?" Gibbs asked, sipping from his coffee.

"There were actually two types of hair and unfortunately they belong to Ziva and Tony." Ducky said. Every eye turned to stare at them.

"What the hell have you been doing near radioactive sites?" Gibbs asked them.

"What the hell indeed." Vance said from the staircase leading to the next floor. Tony and Ziva looked at each other and then Tony told them what happened.


	3. Chapter 3

**I know that this is a short chapter, but i am really busy at the moment. I will post the next one as soon as possible though.**

"A few days ago, we stopped the plane to get some more supplies. We happened to be about 13 km's from a radioactive site. A bodyguard and I were walking in that direction to check it out when we heard gunshots. We took our guns out and ran towards where the gunshots had sounded from and found that one of the people that was after Ziva and I had killed a navy captain. We gunned down the killer, but by the time we got to the captain there was nothing we could do.

" He was still awake and his last words where to get him as away from the radioactive plant as we could. I picked him up once he was dead and me and the bodyguard caught a taxi and took him as far away as we could think of. We then turned around and headed back to the plane. I pulled some of my hair out when it got caught on his button. Ziva's hair was probably on him because she had fallen asleep on the shoulder that I carried on." Tony recounted.

Everyone looked shocked.

"Boss, does that mean that he and that bodyguard were witnesses?" McGee asked Gibbs.

"Yes, it does." Gibbs said.

Just as he said that, the bodyguard that had been with Tony stumbled in and was holding his stomach. When he got to Tony, he removed his hand to reveal a small gash running across his stomach.

"I shot him. He didn't cut me deep, but I feel woozy." He said. Ziva stood up and sat him down. Ducky came over and checked him out.

"That can be fixed with some bandages. Come downstairs to my ER. I will clean that up for you." Ducky said. The bodyguard stood up and followed Ducky and Palmer to the elevator to get to the ER, located in the basement of the building.

"Why didn't you call as soon as this happened?" Vance asked once he had travelled down the last flight of stairs and had reached the others.

"We couldn't. We're being chased and we didn't want to lead them to you." Tony said. He cared about his friends and family and he didn't want any of them to suffer for them.

"You still should've called." Vance said, slightly raising his voice.

"He didn't have a choice. I dumped our phones after we first started being followed and then I pulled out the one the plane. If the people following us had managed to get the flight details, I wasn't going to take any chances." Ziva said back. She was getting angry with Vance for sending her on the mission in the first place.

"You could have bought a burn phone." Vance said, slightly louder than last time.

"No we couldn't. There was always someone watching our every move. That's why we came here." Ziva yelled at Vance.

"I don't care if you're being followed. You should have called us to tell us about what had happened." Vance had rarely raised his voice at the team before so they knew that he was mad.

Ziva yelled something in Israeli, letting her emotion come out all in one. McGee had been learning Israeli for that reason so he could translate so when Ziva said that she was pregnant, his eyes widened.

"What?" Tony asked him when McGee wouldn't stop staring at him.

McGee walked over to him and Ziva and pulled them away from the group so he could talk to them in private.

"You're pregnant?" McGee asked Ziva when they were quite far away from everyone.

"How did you know?" She asked, her anger suddenly all gone.

"I've been taking lessons speaking Israeli so when you said something like that I could translate for everyone. You should be glad I hadn't started translating it to Gibbs." McGee said to them.

"You can't tell anyone." Tony told McGee. McGee nodded and then went back to the group.

"What was that about?" Abby asked him. McGee just shook his head and sat down at his desk. He then pulled his phone out of his pocket and texted Abby saying that he would tell her later.

No one except knew this, but he was in love with Abby. He had been for some time now, but because Gibbs had a rule about not dating co-workers, he had never done anything about it, but since Tony and Ziva broke that rule he was going to as well. Today was the day he told Abby Scuito that he loved her.


End file.
